[English] 日本語
Yorodumi- PDB-3sx6: Crystal structure of sulfide:quinone oxidoreductase Cys356Ala var... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sx6 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of sulfide:quinone oxidoreductase Cys356Ala variant from Acidithiobacillus ferrooxidans complexed with decylubiquinone | |||||||||
Components | Sulfide-quinone reductaseSulfide:quinone reductase | |||||||||
Keywords | OXIDOREDUCTASE / sulfide:quinone oxidoreductase / Cys356Ala variant / integral monotopic membrane protein / complex with sulfide and decylubiquinone | |||||||||
Function / homology | Function and homology information bacterial sulfide:quinone reductase / sulfide:quinone oxidoreductase activity / quinone binding / nucleotide binding / membrane Similarity search - Function | |||||||||
Biological species | Acidithiobacillus ferrooxidans ATCC 23270 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7955 Å | |||||||||
Authors | Cherney, M.M. / Zhang, Y. / James, M.N.G. / Weiner, J.H. | |||||||||
Citation | Journal: J.Struct.Biol. / Year: 2012 Title: Structure-activity characterization of sulfide:quinone oxidoreductase variants. Authors: Cherney, M.M. / Zhang, Y. / James, M.N. / Weiner, J.H. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3sx6.cif.gz | 188.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3sx6.ent.gz | 148.1 KB | Display | PDB format |
PDBx/mmJSON format | 3sx6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sx/3sx6 ftp://data.pdbj.org/pub/pdb/validation_reports/sx/3sx6 | HTTPS FTP |
---|
-Related structure data
Related structure data | 3sxiC 3sy4C 3syiC 3sz0C 3szcC 3szfC 3szwC 3t0kC 3t14C 3t2kC 3t2yC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
|
-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 47798.023 Da / Num. of mol.: 1 / Mutation: C356A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acidithiobacillus ferrooxidans ATCC 23270 (bacteria) Strain: ATCC 23270 / DSM 14882 / NCIB 8455 / Gene: AFE_1792 / Production host: Escherichia coli (E. coli) References: UniProt: B7JBP8, bacterial sulfide:quinone reductase |
---|---|
#3: Sugar | ChemComp-LMT / |
-Non-polymers , 5 types, 347 molecules
#2: Chemical | ChemComp-FAD / | ||||
---|---|---|---|---|---|
#4: Chemical | ChemComp-DCQ / | ||||
#5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.54 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 30% PEG 600, 0.1 M bis-tris buffer,0.1 M MgSO4, 0.05% DDM, 2 mM decylubiquinone, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 11, 2009 |
Radiation | Monochromator: DCM, Si(111) cryo-cooled first crystal and sagittally bent second Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.7955→50 Å / Num. all: 50553 / Num. obs: 46610 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.8 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 32.2 |
Reflection shell | Resolution: 1.7955→1.86 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.749 / Mean I/σ(I) obs: 1.83 / Num. unique all: 3202 / Rsym value: 0.749 / % possible all: 64.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7955→30.14 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 24.6 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.235 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7955→30.14 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|